🦠 Amplicon 16S

qiime2.sh

Preprocess
Quality control & filtering
Assign taxonomy
Diversity analysis
Phylogenetic tree

Create visualizations

R - qiimer2, phyloseq & metagenomeSeq

Sample composition plots
Alpha & Beta diversity
Differential abundance analysis (for zero inflated data)

Python - Microbiome gene set enrichment

Microbiome set enrichment analysis with MSEA
Pathways enrichment analysis with GSEApy